From c9cd5def9129d230c611cfc1ac88679fe5700cdd Mon Sep 17 00:00:00 2001 From: Mathieu Giraud Date: Wed, 19 Jan 2022 09:25:06 +0100 Subject: [PATCH 1/5] vidjil-algo: pride, 2022 --- algo/core/bam.cpp | 4 ++-- algo/core/bioreader.cpp | 4 ++-- algo/core/bioreader.hpp | 4 ++-- algo/core/cluster-junctions.cpp | 4 ++-- algo/core/compare-all.cpp | 4 ++-- algo/core/dynprog.cpp | 4 ++-- algo/core/fasta.cpp | 4 ++-- algo/core/kmeraffect.cpp | 4 ++-- algo/core/kmerstore.cpp | 4 ++-- algo/core/segment.cpp | 4 ++-- algo/core/similarityMatrix.cpp | 4 ++-- algo/vidjil.cpp | 4 ++-- 12 files changed, 24 insertions(+), 24 deletions(-) diff --git a/algo/core/bam.cpp b/algo/core/bam.cpp index cdec85f5d..497177b04 100644 --- a/algo/core/bam.cpp +++ b/algo/core/bam.cpp @@ -1,6 +1,6 @@ /* - This file is part of Vidjil - Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics + This file is part of Vidjil-algo + Copyright (C) 2011-2022 by VidjilNet consortium and Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille Contributors: Mathieu Giraud diff --git a/algo/core/bioreader.cpp b/algo/core/bioreader.cpp index 1a094d6ee..ea9ce9a96 100644 --- a/algo/core/bioreader.cpp +++ b/algo/core/bioreader.cpp @@ -1,6 +1,6 @@ /* - This file is part of Vidjil - Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics + This file is part of Vidjil-algo + Copyright (C) 2011-2022 by VidjilNet consortium and Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille Contributors: Mathieu Giraud diff --git a/algo/core/bioreader.hpp b/algo/core/bioreader.hpp index 32c96e86d..683adbdfd 100644 --- a/algo/core/bioreader.hpp +++ b/algo/core/bioreader.hpp @@ -1,6 +1,6 @@ /* - This file is part of Vidjil - Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics + This file is part of Vidjil-algo + Copyright (C) 2011-2022 by VidjilNet consortium and Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille Contributors: Mathieu Giraud diff --git a/algo/core/cluster-junctions.cpp b/algo/core/cluster-junctions.cpp index 4ffa9052b..da7b0deb2 100644 --- a/algo/core/cluster-junctions.cpp +++ b/algo/core/cluster-junctions.cpp @@ -1,6 +1,6 @@ /* - This file is part of Vidjil - Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics + This file is part of Vidjil-algo + Copyright (C) 2011-2022 by VidjilNet consortium and Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille Contributors: Mathieu Giraud diff --git a/algo/core/compare-all.cpp b/algo/core/compare-all.cpp index fdfb685a2..092cb4b80 100644 --- a/algo/core/compare-all.cpp +++ b/algo/core/compare-all.cpp @@ -1,6 +1,6 @@ /* - This file is part of Vidjil - Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics + This file is part of Vidjil-algo + Copyright (C) 2011-2022 by VidjilNet consortium and Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille Contributors: Mathieu Giraud diff --git a/algo/core/dynprog.cpp b/algo/core/dynprog.cpp index 586392aeb..7f596999e 100644 --- a/algo/core/dynprog.cpp +++ b/algo/core/dynprog.cpp @@ -1,6 +1,6 @@ /* - This file is part of Vidjil - Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics + This file is part of Vidjil-algo + Copyright (C) 2011-2022 by VidjilNet consortium and Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille Contributors: Mathieu Giraud diff --git a/algo/core/fasta.cpp b/algo/core/fasta.cpp index 1a8ed7a70..288b4e798 100644 --- a/algo/core/fasta.cpp +++ b/algo/core/fasta.cpp @@ -1,6 +1,6 @@ /* - This file is part of Vidjil - Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics + This file is part of Vidjil-algo + Copyright (C) 2011-2022 by VidjilNet consortium and Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille Contributors: Mathieu Giraud diff --git a/algo/core/kmeraffect.cpp b/algo/core/kmeraffect.cpp index edc0d98c6..235429e83 100644 --- a/algo/core/kmeraffect.cpp +++ b/algo/core/kmeraffect.cpp @@ -1,6 +1,6 @@ /* - This file is part of Vidjil - Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics + This file is part of Vidjil-algo + Copyright (C) 2011-2022 by VidjilNet consortium and Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille Contributors: Mathieu Giraud diff --git a/algo/core/kmerstore.cpp b/algo/core/kmerstore.cpp index 235e41408..7da0ee075 100644 --- a/algo/core/kmerstore.cpp +++ b/algo/core/kmerstore.cpp @@ -1,6 +1,6 @@ /* - This file is part of Vidjil - Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics + This file is part of Vidjil-algo + Copyright (C) 2011-2022 by VidjilNet consortium and Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille Contributors: Mathieu Giraud diff --git a/algo/core/segment.cpp b/algo/core/segment.cpp index 30a4080ad..7c38c7f36 100644 --- a/algo/core/segment.cpp +++ b/algo/core/segment.cpp @@ -1,6 +1,6 @@ /* - This file is part of Vidjil - Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics + This file is part of Vidjil-algo + Copyright (C) 2011-2022 by VidjilNet consortium and Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille Contributors: Mathieu Giraud diff --git a/algo/core/similarityMatrix.cpp b/algo/core/similarityMatrix.cpp index 0a5f4eeed..0f3d58b6f 100644 --- a/algo/core/similarityMatrix.cpp +++ b/algo/core/similarityMatrix.cpp @@ -1,6 +1,6 @@ /* - This file is part of Vidjil - Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics + This file is part of Vidjil-algo + Copyright (C) 2011-2022 by VidjilNet consortium and Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille Contributors: Mathieu Giraud diff --git a/algo/vidjil.cpp b/algo/vidjil.cpp index 21e3d2ef7..7a4727e23 100644 --- a/algo/vidjil.cpp +++ b/algo/vidjil.cpp @@ -1,6 +1,6 @@ /* This file is part of Vidjil-algo - Copyright (C) 2011-2021 by VidjilNet consortium and Bonsai bioinformatics + Copyright (C) 2011-2022 by VidjilNet consortium and Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille Contributors: Mathieu Giraud @@ -210,7 +210,7 @@ string string_NO_LIMIT(string s) int main (int argc, char **argv) { cout << "# " << PROGNAME << " -- V(D)J recombinations analysis " << endl - << "# Copyright (C) 2011-2021 by the Vidjil team" << endl + << "# Copyright (C) 2011-2022 by the Vidjil team" << endl << "# Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille" << endl << "# VidjilNet consortium" << endl << endl -- GitLab From d52952bb819dffe28da71a0bf7fef8a16f435a6f Mon Sep 17 00:00:00 2001 From: Mathieu Giraud Date: Wed, 19 Jan 2022 09:34:19 +0100 Subject: [PATCH 2/5] browser: pride, 2022 --- browser/js/autocomplete.js | 2 +- browser/js/axis.js | 2 +- browser/js/axis_conf.js | 2 +- browser/js/builder.js | 2 +- browser/js/clone.js | 2 +- browser/js/com.js | 4 ++-- browser/js/dbscan.js | 2 +- browser/js/germline_builder.js | 2 +- browser/js/graph.js | 2 +- browser/js/indexedDom.js | 2 +- browser/js/info.js | 2 +- browser/js/list.js | 2 +- browser/js/main.js | 2 +- browser/js/menu.js | 2 +- browser/js/model.js | 2 +- browser/js/model_loader.js | 2 +- browser/js/scatterPlot.js | 2 +- browser/js/scatterPlot_menu.js | 2 +- browser/js/scatterPlot_selector.js | 2 +- browser/js/screen_MRD.js | 2 +- browser/js/shortcut.js | 2 +- browser/js/tokeniser.js | 2 +- browser/js/vidjil-style.js | 2 +- browser/js/view.js | 2 +- 24 files changed, 25 insertions(+), 25 deletions(-) diff --git a/browser/js/autocomplete.js b/browser/js/autocomplete.js index 721446cb0..a9200b57c 100644 --- a/browser/js/autocomplete.js +++ b/browser/js/autocomplete.js @@ -1,6 +1,6 @@ /* This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/axis.js b/browser/js/axis.js index 4504bd43c..515a7c164 100644 --- a/browser/js/axis.js +++ b/browser/js/axis.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2020 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/axis_conf.js b/browser/js/axis_conf.js index 7f0b8b08e..7d8613bdf 100644 --- a/browser/js/axis_conf.js +++ b/browser/js/axis_conf.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/builder.js b/browser/js/builder.js index 3cc09ef5e..8ff09710b 100644 --- a/browser/js/builder.js +++ b/browser/js/builder.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/clone.js b/browser/js/clone.js index 64332a38f..39afd3b1d 100644 --- a/browser/js/clone.js +++ b/browser/js/clone.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/com.js b/browser/js/com.js index 197425e2e..d2a0b5d7d 100644 --- a/browser/js/com.js +++ b/browser/js/com.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez @@ -87,7 +87,7 @@ function Com(default_console) { BUTTON_CLOSE_POPUP, "welcome": "

Vidjil

" + - "(c) 2011-2021, The Vidjil Team: " + + "(c) 2011-2022, The Vidjil Team: " + "Aurélien Béliard, Marc Duez, Mathieu Giraud, Ryan Herbert, Mikaël Salson, Tatiana Rocher and Florian Thonier" + " – http://www.vidjil.org/" + (typeof git_sha1 !== "undefined" ? " – " + git_sha1 : "") + diff --git a/browser/js/dbscan.js b/browser/js/dbscan.js index ae968dd69..0c676e170 100644 --- a/browser/js/dbscan.js +++ b/browser/js/dbscan.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Antonette Carin diff --git a/browser/js/germline_builder.js b/browser/js/germline_builder.js index 10238ffb5..1c5369632 100644 --- a/browser/js/germline_builder.js +++ b/browser/js/germline_builder.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/graph.js b/browser/js/graph.js index e0a56f4b8..f4725e63b 100644 --- a/browser/js/graph.js +++ b/browser/js/graph.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/indexedDom.js b/browser/js/indexedDom.js index dbad1181d..5172838ed 100644 --- a/browser/js/indexedDom.js +++ b/browser/js/indexedDom.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/info.js b/browser/js/info.js index 1e27f238c..cc092249d 100644 --- a/browser/js/info.js +++ b/browser/js/info.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/list.js b/browser/js/list.js index c8af70d7f..e9d80d301 100644 --- a/browser/js/list.js +++ b/browser/js/list.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2017 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/main.js b/browser/js/main.js index a24c614b9..ddd26056e 100644 --- a/browser/js/main.js +++ b/browser/js/main.js @@ -1,6 +1,6 @@ /* This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/menu.js b/browser/js/menu.js index ab57d5ecc..8eb1e06de 100644 --- a/browser/js/menu.js +++ b/browser/js/menu.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/model.js b/browser/js/model.js index fac10c383..0a4be5295 100644 --- a/browser/js/model.js +++ b/browser/js/model.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/model_loader.js b/browser/js/model_loader.js index d3b9fd54c..f2978ae08 100644 --- a/browser/js/model_loader.js +++ b/browser/js/model_loader.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/scatterPlot.js b/browser/js/scatterPlot.js index 750c9e0af..a0fafd04f 100644 --- a/browser/js/scatterPlot.js +++ b/browser/js/scatterPlot.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/scatterPlot_menu.js b/browser/js/scatterPlot_menu.js index 8b864d7c2..763b0c6b3 100644 --- a/browser/js/scatterPlot_menu.js +++ b/browser/js/scatterPlot_menu.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/scatterPlot_selector.js b/browser/js/scatterPlot_selector.js index e786175cc..c35b57296 100644 --- a/browser/js/scatterPlot_selector.js +++ b/browser/js/scatterPlot_selector.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/screen_MRD.js b/browser/js/screen_MRD.js index 14c2a8f4e..d7a621566 100644 --- a/browser/js/screen_MRD.js +++ b/browser/js/screen_MRD.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2020 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Joao Meidanis diff --git a/browser/js/shortcut.js b/browser/js/shortcut.js index 7f6c5ec43..f3680e320 100644 --- a/browser/js/shortcut.js +++ b/browser/js/shortcut.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Antonin Carette diff --git a/browser/js/tokeniser.js b/browser/js/tokeniser.js index c5f821661..c7bd1d42b 100644 --- a/browser/js/tokeniser.js +++ b/browser/js/tokeniser.js @@ -1,6 +1,6 @@ /* This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/vidjil-style.js b/browser/js/vidjil-style.js index 297fa8ff6..facc94b19 100644 --- a/browser/js/vidjil-style.js +++ b/browser/js/vidjil-style.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez diff --git a/browser/js/view.js b/browser/js/view.js index 26230cede..94539f43e 100644 --- a/browser/js/view.js +++ b/browser/js/view.js @@ -1,7 +1,7 @@ /* * This file is part of Vidjil , * High-throughput Analysis of V(D)J Immune Repertoire. - * Copyright (C) 2013-2017 by Bonsai bioinformatics + * Copyright (C) 2013-2022 by VidjilNet consortium and Bonsai bioinformatics * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille * Contributors: * Marc Duez -- GitLab From 66c08c5efb81b779113dc5bf77946c543cc2099c Mon Sep 17 00:00:00 2001 From: Mathieu Giraud Date: Wed, 19 Jan 2022 09:38:11 +0100 Subject: [PATCH 3/5] server: pride, 2022 --- server/web2py/applications/vidjil/models/db.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/server/web2py/applications/vidjil/models/db.py b/server/web2py/applications/vidjil/models/db.py index da2fc5187..cf1c599de 100644 --- a/server/web2py/applications/vidjil/models/db.py +++ b/server/web2py/applications/vidjil/models/db.py @@ -2,7 +2,7 @@ # This file is part of Vidjil , # High-throughput Analysis of V(D)J Immune Repertoire. -# Copyright (C) 2014-2017 by Bonsai bioinformatics +# Copyright (C) 2014-2022 by Bonsai bioinformatics # at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille # # "Vidjil" is free software: you can redistribute it and/or modify -- GitLab From e61d45c04e2a3d3286ea991cf57dfe1b03ad3711 Mon Sep 17 00:00:00 2001 From: Mathieu Giraud Date: Wed, 19 Jan 2022 09:31:16 +0100 Subject: [PATCH 4/5] doc: pride, 2022 --- doc/credits.md | 10 +++++----- doc/vidjil-algo.md | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/doc/credits.md b/doc/credits.md index 83d169d57..020a6d5e8 100644 --- a/doc/credits.md +++ b/doc/credits.md @@ -8,11 +8,11 @@ Contact: [Mathieu Giraud and Mikaël Salson](mailto:contact@vidjil.org) ## Vidjil core development - - Mathieu Giraud, 2011-2021 - - Mikaël Salson, 2011-2021 - - Marc Duez, 2012-2016, 2019-2021 + - Mathieu Giraud, 2011-2022 + - Mikaël Salson, 2011-2022 + - Marc Duez, 2012-2016, 2019-2022 - Tatiana Rocher, 2014-2017 - - Florian Thonier, 2015-2021 + - Florian Thonier, 2015-2022 - Ryan Herbert, 2015-2020 - Aurélien Béliard, 2016-2017 @@ -65,7 +65,7 @@ The development of Vidjil is funded by: - SIRIC ONCOLille (Grant INCa-DGOS-Inserm 6041), 2014-2017 - Inria Lille, 2015-2018 - InCA, 2016-2019 - - VidjilNet consortium at Inria, 2018-2021 + - VidjilNet consortium at Inria, 2018-2022 ## References diff --git a/doc/vidjil-algo.md b/doc/vidjil-algo.md index b506f373c..536dfd2ad 100644 --- a/doc/vidjil-algo.md +++ b/doc/vidjil-algo.md @@ -5,7 +5,7 @@ ``` Vidjil -- High-throughput Analysis of V(D)J Immune Repertoire -- [[http://www.vidjil.org]] - Copyright (C) 2011-2021 by Bonsai bioinformatics + Copyright (C) 2011-2022 by Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille and VidjilNet consortium. contact@vidjil.org -- GitLab From 79fdc4ae1a9c417be33e6ddd9ae9d6c81e81acc2 Mon Sep 17 00:00:00 2001 From: Mathieu Giraud Date: Wed, 19 Jan 2022 09:46:15 +0100 Subject: [PATCH 5/5] doc/roadmap.md: dimers, clonal evolution Follows end-2021 review of most requested features vdj#1300 --- doc/roadmap.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/roadmap.md b/doc/roadmap.md index 7bc7128b9..7e46e9056 100644 --- a/doc/roadmap.md +++ b/doc/roadmap.md @@ -65,6 +65,8 @@ with software engineering. ## Better sequence and recombination analysis + - Detect primer dimers #2820 + - Show more sequence features (such as FR1...) in the sequence aligner #2135 + **Available since Q2 2021**, ✅ @@ -84,7 +86,7 @@ Moreover, we always try to improve and extend the analysis of some recombination - Extend set of recombinations - Find generalized recombinations, even unexpected #1400 #2818 - - Work on clone phylogenies + - Work on clonal evolution #1726, on clone phylogenies - Work on noisy data, such as third-generation sequencers These points are *ongoing research* 🚧 in the Bonsai team with selected collaborators and are not in the roadmap with fixed dates. -- GitLab